GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Caldicellulosiruptor hydrothermalis 108

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate WP_013403459.1 CALHY_RS08000 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::O18404
         (255 letters)



>NCBI__GCF_000166355.1:WP_013403459.1
          Length = 248

 Score =  140 bits (354), Expect = 2e-38
 Identities = 92/259 (35%), Positives = 140/259 (54%), Gaps = 19/259 (7%)

Query: 1   MIKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKE----LGDKVVFVP 56
           ++K+ V+L+TG + G+GRA A + A+ GA+VI+    S    E  KE    +G K + + 
Sbjct: 3   LLKDKVALITGASRGIGRAIALKFAQNGANVIINYSSSQSQAENLKEEIEKIGTKTMIIK 62

Query: 57  VDVTSEKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININT 116
            DV+S  +V+      + +FGRLD+ VN AG          N+      EDF +VI IN 
Sbjct: 63  CDVSSADEVNQMFSQVEKEFGRLDILVNNAGITKDGLILRMNE------EDFDKVIAINL 116

Query: 117 VGTFNVIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPI 176
            G F   R +A +M         + G I+N +SV    G +GQA Y+ASKA ++G+T  +
Sbjct: 117 KGAFLCARAAARMMVKQ------RFGNIINISSVVGIAGNVGQANYAASKAGIIGLTKSL 170

Query: 177 ARDLSTQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAH--LVQAI 234
           A++L+++ IR+  IAPG   T M   L +KV+  +  SIP   R GE  E A+  L  A 
Sbjct: 171 AKELASRNIRVNAIAPGFIKTDMTEVLSDKVKEAMLSSIPL-GRFGEADEVANVALFLAS 229

Query: 235 YENPLLNGEVIRIDGALRM 253
             +  + G+VI +DG + M
Sbjct: 230 SLSSYITGQVIVVDGGMIM 248


Lambda     K      H
   0.317    0.133    0.369 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 159
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory